On 6/4/13 12:17 PM, tarak karmakar wrote:
Thanks Justin.
Sorry for not uploading the full .mdp. Here it is,
; 7.3.3 Run Control
integrator = md
tinit = 0
dt = 0.001
nsteps = 5000000
nstcomm = 1
comm_grps = system
comm_mode = linear
energygrps = system
; 7.3.8 Output Control
nstxout = 5000
nstfout = 5000
nstlog = 1000
nstenergy = 1000
nstxtcout = 1000
xtc_precision = 1000
xtc_grps = System
; 7.3.9 Neighbor Searching
nstlist = 10
ns_type = grid
pbc = xyz
rlist = 1.2
rlistlong = 1.4
; 7.3.10 Electrostatics
coulombtype = PME
rcoulomb = 1.2
fourierspacing = 0.12
pme_order = 4
ewald_rtol = 1e-5
; 7.3.11 VdW
vdwtype = switch
rvdw = 1.2
rvdw-switch = 1.0
DispCorr = Ener
; 7.3.14 Temperature Coupling
tcoupl = nose-hoover
tc_grps = system
tau_t = 1.0
ref_t = 300
; 7.3.15 Pressure Coupling
pcoupl = parrinello-rahman
pcoupltype = isotropic
tau_p = 1.0
compressibility = 4.5e-5
ref_p = 1.0
gen_vel = yes
gen_temp = 300
gen_seed = 93873959697
; 7.3.18 Bonds
constraints = h-bonds
constraint_algorithm = LINCS
continuation = yes
lincs_order = 4
lincs_iter = 1
lincs_warnangle = 30
Note: Using CHARMM27 force field
I didn't use the 'continuation' part here.
In the heating run I didn't put any constraints but in the production MD, I
do apply constraints to the covalent bonds involving hydrogens. I just want
The introduction of constraints explains the observed behavior. You ran an
unconstrained simulation, then at step 0 of the constrained simulation, the
constraints have to be satisfied, which may introduce sudden movement in atomic
positions, hence large velocities and a high temperature. The rule of thumb I
always use - if you're going to use constraints during production simulations,
use constraints during equilibration. I have seen several instances where
unconstrained equilibration causes constrained simulations to later fail.
to test the ligand movement inside the protein cavity in different set of
initial velocities to get the feelings of how ligand is interacting with
certain residues.
So, then should I use these different velocity generating seeds during the
warm up step?
That's an interesting question. If you're warming from 0 -> 300 K, I don't know
how grompp will generate velocities at 0 K, but regenerating velocities after
warming seems to defeat the purpose of doing the warming at all, in my mind,
since you're just going to re-randomize the entire system by doing so.
-Justin
--
========================================
Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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